/*
 * Copyright (c) 2017 NCIC, Institute of Computing Technology, Chinese Academy of Sciences
 *
 * Permission is hereby granted, free of charge, to any person obtaining a copy
 * of this software and associated documentation files (the "Software"), to deal
 * in the Software without restriction, including without limitation the rights
 * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the Software is
 * furnished to do so, subject to the following conditions:
 *
 * The above copyright notice and this permission notice shall be included in
 * all copies or substantial portions of the Software.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 * THE SOFTWARE.
 */
package org.ncic.bioinfo.sparkseq.fileio

import org.apache.spark.SparkContext
import org.apache.spark.rdd.RDD
import org.ncic.bioinfo.sparkseq.data.basic.{BasicSamRecord, FastqPairRecord, FastqRecord, VcfRecord}
import org.ncic.bioinfo.sparkseq.data.common.{RefContigInfo, VcfHeaderInfo}

/**
  * Author: wbc
  */
trait FileLoader {

  def loadFastq(filePath: String): List[FastqRecord]

  def loadFastqToRdd(sc: SparkContext, filePath: String): RDD[FastqRecord]

  def loadFastqPair(filePath1: String, filePath2: String): List[FastqPairRecord]

  def loadFastqPairToRdd(sc: SparkContext, filePath1: String, filePath2: String): RDD[FastqPairRecord]

  def loadSam(filePath: String, refContigInfo: RefContigInfo): List[BasicSamRecord]

  def loadSamToRdd(sc: SparkContext, filePath: String, refContigInfo: RefContigInfo): RDD[BasicSamRecord]

  def loadVcf(filePath: String, refContigInfo: RefContigInfo): List[VcfRecord]

  def loadVcfToRdd(sc: SparkContext, filePath: String, refContigInfo: RefContigInfo): RDD[VcfRecord]

  def loadVcfHeader(filePath: String): VcfHeaderInfo

}
